Re: [Ifeffit] EXAFS simulations

Ciao Sebastiano, did you use the mu-column of the xmu.dat? If so, the main difference between the chi.dat and the xmu.dat is that the mue_0 (as calculated by FEFF) is already subtracted in the former while it needs to be subtracted by Athena in the latter. Some of the difficulties you mentioned are thus due to problems of Athena to do a decent background (i.e. mue_0 and normalization) processing if there is no pre-edge region. Thus the effect of changing the absorption energy in Cu Bulk 4 from 8988.430eV to 8988.431eV is not caused by a *wrong* Enot but by a change in the edge-jump of almost 50% (due to a different *pre-edge*). Thus using the chi.dat seems to be the better (i.e. more reproducible) choice in this case (a precautionary note though: the mue_0 as calculated by FEFF will most likely differ between the central and the peripheral atoms; this may be part of the cluster-effect or an artifact (I assume that this is only a problem in the XANES region but I don't know, so you should check this by plotting the single mue_0). HTH Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of ifeffit-request@millenia.cars.aps.anl.gov Sent: Fri 10/24/2008 09:57 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 68, Issue 21 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Fit XANES spectra using Athena (Adam Webb) 2. EXAFS simulations (Cammelli Sebastiano) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Oct 2008 07:39:55 +0200 From: Adam Webb Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: XAFS Analysis using Ifeffit Message-ID: <49015FAB.5060802@desy.de> Content-Type: text/plain; charset=ISO-8859-1 Hi Jenny, I don't know what exactly you are trying to do so I can't say which method is better but I can make a comment. It all comes down to the number of independent variables. The Gaussian and step functions are independent of each other. The heights, widths and positions can all be adjusted. In the linear combination you change everything together so for example, the ratio of the peak height and the step height doesn't change. The result is that you need more spectra to get the same number of degrees of freedom as in the least-squares peak fit. Cheers, Adam Jenny Cai wrote:

Hello everyone,

Sorry for bothering you again.

I am using least-squares peak fit and linear combination fit to analyze my samples. I have spent tons of time on it, and it really makes me crazy. Why can't I get consistent results from these two methods?

Please see the attached file. Both of these methods work well individually, but linear combination fit always need more peaks than peak fit to get an 'ok' fitting. Should I stick on one method for all my samples, no matter what results the other one gives? It is confusing me so much. Could anyone help me out?

Thank you in advance for your help!

Jenny

------------------------------ Message: 2 Date: Fri, 24 Oct 2008 09:57:35 +0200 From: "Cammelli Sebastiano" Subject: [Ifeffit] EXAFS simulations To: Message-ID: Content-Type: text/plain; charset="us-ascii" Dear IFFEFIT user I do some EXAFS simulations (FEFF8.4) of small pure Cu clusters (fcc bulk structure) and then I try to compare them with experimental data. The simulations are performed on all the shells, then all the contribution are added according to the number of atoms per shell (so the total xmu of a cluster of 19 atoms is = [xmu0+12*xmu1+6*xmu2]/19 where xmu0 is the xmu of the atom in the center of the cluster and xmu1 of the atoms in the first shell and xmu2 for the second shell). The first and obvious result concerns the peaks amplitude of the FT which is proportional to the number of atoms involved in the simulations. I have calculated the EXAFS spectra from the xmu.dat files. As you know in EXAFS simulations there is not pre-edge so finally is not easy to find the right value of E0. In the Athena.prj file I attached you can easily see this effect changing the absorption energy of Cu Bulk 4 from 8988.430eV to 8988.431eV. The amplitude of the first peak of the FT changes from 100 to 60! In order to overcome this problem I recalculated the FT using the chi.dat and not the xmu.dat. In the Athena file you can find the 8 simulations based on the xmu.dat (and they are called Cu bulk 1.... Cu bulk 8) and on the chi.dat (called CHI_Cu bulk 1....8). Of course they refer to the same cluster and they were calculated in the same way. Since these simulations, calculated on the Chi.dat, are very different from those calculated on xmu.dat, some questions rise. Moreover if you compare the FT of the simulations Chi_Cu bulk 5 and Chi_Cu Bulk 6 you can see that the amplitude of the first peak is larger for the smaller cluster. 1. Should I use the spectra I got from the xmu.dat or from the chi.dat? 2. Are the difference between Chi_Cu 5 and Chi Cu 6 (even if small) due to the E0 calculation? 3. How shall I behave if the first derivative of some simulations does not show a peak where it is "reasonably" expected (compare Cu Bulk 4 and Cu Bulk 7) 4. Do you have any other suggestions? Thank you in advance for any suggestion, Best regards Sebastiano Cammelli